The haul from Japan's whaling fleet in the Southern Ocean was a "record low" this year, a government minister says, blaming "unforgivable sabotage" by activists.

The hunt netted just 103 Antarctic minke whales, less than half its tally last year and no fin whales, Agriculture, Forestry and Fisheries Minister Yoshimasa Hayashi said on Friday, adding it was the lowest total since "research whaling" began in 1987.

The fleet, which was again harassed by environmentalist group Sea Shepherd, is due to arrive back in Japan between Friday and Sunday, Hayashi told a press conference.

During the 48-day-long whaling expedition, campaigners - labelled "pirates" earlier this year by a US judge - disrupted the hunt four times and the Japanese ships spent 21 days avoiding their vessels, the Fisheries Agency said.

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Sea Shepherd committed "unforgivable sabotage", Hayashi said, according to Kyodo News, including a collision with a whaling vessel as it was being refuelled.

"We will seek more support from other countries to conduct research whaling in a stable manner," the minister said.

Japan's annual whale hunt has long drawn criticism from activists and foreign governments, but Tokyo defends the practice, saying eating whale is part of the country's culinary traditions.

Captured whales, later sold as food, are studied as part of a bid by Japan's whaling research institute to prove the mammals' populations can sustain commercial whaling, but activists charge Tokyo uses a loophole to get around an international ban on hunting.

Norway and Iceland are the only nations that hunt whales in open defiance of a 1986 moratorium on commercial whaling.

Japan's whaling fleet left port in December aiming to catch about 1000 whales.